1---2name: varcadd-pathogenicity3description: Variant Scorer4license: Non-Commercial5---67<!--8# COPYRIGHT NOTICE9# This file is part of the "Universal Biomedical Skills" project.10# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>11# All Rights Reserved.12#13# This code is proprietary and confidential.14# Unauthorized copying of this file, via any medium is strictly prohibited.15#16# Provenance: Authenticated by MD BABU MIA1718-->192021# varCADD (Variant Pathogenicity Predictor)2223Genome-wide pathogenicity prediction leveraging standing variation data to improve accuracy over traditional CADD scores.2425## When to Use2627* **Variant Prioritization**: Ranking candidate variants in rare disease cases.28* **VUS Interpretation**: Assessing variants of uncertain significance.29* **Research**: Annotating novel variants in population studies.3031## Core Capabilities32331. **Score Generation**: Calculate C-scores for SNVs and indels.342. **Annotation**: Add functional context (conservation, protein domains).353. **Filtering**: Identify likely pathogenic variants based on thresholds.3637## Workflow38391. **Input**: VCF file.402. **Annotate**: Run varCADD model.413. **Filter**: Keep variants with Score > X.424. **Output**: Annotated VCF or ranked table.4344## Example Usage4546**User**: "Score these variants from patient X."4748**Agent Action**:49```bash50varcadd score --input patient.vcf --output scored.vcf51```525354<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add fridrichmethod/varcadd-pathogenicity in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
Variant Scorer It is listed under Coding & Dev Tools on SkillMD.
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